Locus 2282

Sequence ID	X_DroMel_CAF1
Location	6,165,788 – 6,165,914
Length	126
Max. P	0.999674

overview

Window 7

Location	6,165,788 – 6,165,887
Length	99
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	86.70
Mean single sequence MFE	-26.54
Consensus MFE	-22.74
Energy contribution	-23.14
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.85
Structure conservation index	0.86
SVM decision value	1.12
SVM RNA-class probability	0.917724
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6165788 99 + 22224390
CCGGCGGCAUAGAAGCACCCAGCAUAGCCAAUGCAUCCGCAACCUCAACUGCAUCCGCAUCCGCAUUAGCAAAUGCAAGUACAGCCGCCUCCGCAUCCG-
..((((((...((.((.....((((.....))))....(((........)))....)).)).(((((....))))).......))))))..........- ( -27.90)
>DroSec_CAF1 4399 87 + 1
CCGGCGGCAUAGAAGCACCCAGCAUAGCCAAUGCAUCCGC------------AUCUGCAUCCGCAUUAGCAAAUGCAAGUACAGCCGCCUCCGCAUCCG-
..((((((..(((.((.....((((.....))))....))------------.)))((((..((....))..)))).......))))))..........- ( -26.10)
>DroSim_CAF1 6715 87 + 1
CCGGCGGCAUAGAAGCACCCAGCAUAGCCAAUGCAUCCGC------------AUCUGCAUCCGCAUUAGCAAAUGCAAGUACAGCCGCCUCCGCAUCCG-
..((((((..(((.((.....((((.....))))....))------------.)))((((..((....))..)))).......))))))..........- ( -26.10)
>DroEre_CAF1 4263 81 + 1
CCGGCGGCAUUGAAGCACCUAGCAUAGCCGCUGCAUCC------------------GCAUCCGCAUUGGCAAAUGCAAGUACAGCCGCCUCCGCAUCCG-
..((((((......((.....))...((((.(((....------------------......))).)))).............))))))..........- ( -24.60)
>DroYak_CAF1 10055 94 + 1
CCGGCGGCAUUGAAGCACCCAGCAUAGCCACUGCAUCUGCAUCC------GCAUCCGCAUCUGCAUUAGCAAAUGCAAGUACAGCCGCCUCCGCAUCCGC
..((((((......((.....))...((...(((....)))...------))....((((.(((....))).)))).......))))))........... ( -28.00)
>consensus
CCGGCGGCAUAGAAGCACCCAGCAUAGCCAAUGCAUCCGC____________AUCCGCAUCCGCAUUAGCAAAUGCAAGUACAGCCGCCUCCGCAUCCG_
..((((((.............((((.....))))......................((((..((....))..)))).......))))))........... (-22.74 = -23.14 +   0.40)

alignment

secondary structure

dotplot

Window 8

Location	6,165,788 – 6,165,887
Length	99
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	86.70
Mean single sequence MFE	-40.42
Consensus MFE	-36.95
Energy contribution	-37.31
Covariance contribution	0.36
Combinations/Pair	1.14
Mean z-score	-2.96
Structure conservation index	0.91
SVM decision value	3.87
SVM RNA-class probability	0.999674
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6165788 99 - 22224390
-CGGAUGCGGAGGCGGCUGUACUUGCAUUUGCUAAUGCGGAUGCGGAUGCAGUUGAGGUUGCGGAUGCAUUGGCUAUGCUGGGUGCUUCUAUGCCGCCGG
-..........((((((.((((((((((..(((((((((..(((((...(....)...)))))..))))))))).)))).))))))......)))))).. ( -42.40)
>DroSec_CAF1 4399 87 - 1
-CGGAUGCGGAGGCGGCUGUACUUGCAUUUGCUAAUGCGGAUGCAGAU------------GCGGAUGCAUUGGCUAUGCUGGGUGCUUCUAUGCCGCCGG
-..........((((((.((((((((((..(((((((((..(((....------------)))..))))))))).)))).))))))......)))))).. ( -41.00)
>DroSim_CAF1 6715 87 - 1
-CGGAUGCGGAGGCGGCUGUACUUGCAUUUGCUAAUGCGGAUGCAGAU------------GCGGAUGCAUUGGCUAUGCUGGGUGCUUCUAUGCCGCCGG
-..........((((((.((((((((((..(((((((((..(((....------------)))..))))))))).)))).))))))......)))))).. ( -41.00)
>DroEre_CAF1 4263 81 - 1
-CGGAUGCGGAGGCGGCUGUACUUGCAUUUGCCAAUGCGGAUGC------------------GGAUGCAGCGGCUAUGCUAGGUGCUUCAAUGCCGCCGG
-(((..(((..(((.((((((..(((((((((....))))))))------------------)..)))))).))).)))..(((........))).))). ( -36.70)
>DroYak_CAF1 10055 94 - 1
GCGGAUGCGGAGGCGGCUGUACUUGCAUUUGCUAAUGCAGAUGCGGAUGC------GGAUGCAGAUGCAGUGGCUAUGCUGGGUGCUUCAAUGCCGCCGG
.(((..(((..(((.((((((.((((((((((...(((....)))...))------)))))))).)))))).))).)))..(((........))).))). ( -41.00)
>consensus
_CGGAUGCGGAGGCGGCUGUACUUGCAUUUGCUAAUGCGGAUGCAGAU____________GCGGAUGCAUUGGCUAUGCUGGGUGCUUCUAUGCCGCCGG
...........((((((.((((((((((..(((((((((..(((................)))..))))))))).)))).))))))......)))))).. (-36.95 = -37.31 +   0.36)

alignment

secondary structure

dotplot

Window 9

Location	6,165,812 – 6,165,914
Length	102
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	83.83
Mean single sequence MFE	-35.26
Consensus MFE	-25.30
Energy contribution	-25.62
Covariance contribution	0.32
Combinations/Pair	1.12
Mean z-score	-2.20
Structure conservation index	0.72
SVM decision value	0.99
SVM RNA-class probability	0.896385
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6165812 102 - 22224390
ACGACGAUGAGGAGGAGGCGGAUGCUG---------CGGAUGCGGAGGCGGCUGUACUUGCAUUUGCUAAUGCGGAUGCGGAUGCAGUUGAGGUUGCGGAUGCAUUGGCUA
.(..(.....)..)..(((.(((((..---------....(((((...((((((((..(((((((((....)))))))))..))))))))...)))))...))))).))). ( -40.40)
>DroSec_CAF1 4423 90 - 1
ACGACGAGGAGGAGGAGGCGGAUGCUG---------CGGAUGCGGAGGCGGCUGUACUUGCAUUUGCUAAUGCGGAUGCAGAU------------GCGGAUGCAUUGGCUA
.(..(.....)..)..(((.(((.(((---------(....))))..(((.(((((.((((((((((....)))))))))).)------------)))).)))))).))). ( -32.10)
>DroSim_CAF1 6739 90 - 1
ACGACGAGGAGGAGGAGGCGGAUGCUG---------CGGAUGCGGAGGCGGCUGUACUUGCAUUUGCUAAUGCGGAUGCAGAU------------GCGGAUGCAUUGGCUA
.(..(.....)..)..(((.(((.(((---------(....))))..(((.(((((.((((((((((....)))))))))).)------------)))).)))))).))). ( -32.10)
>DroEre_CAF1 4287 84 - 1
ACGACGAGGAUGAGGAGGCGGAUGCUG---------CGGAUGCGGAGGCGGCUGUACUUGCAUUUGCCAAUGCGGAUGC------------------GGAUGCAGCGGCUA
.(..((....((....(((....))).---------))....))..)((.((((((..(((((((((....))))))))------------------)..)))))).)).. ( -31.50)
>DroYak_CAF1 10079 105 - 1
ACGACGACGAGGAGGAGGCAGAUGCUGCGGAUGUUGCGGAUGCGGAGGCGGCUGUACUUGCAUUUGCUAAUGCAGAUGCGGAUGC------GGAUGCAGAUGCAGUGGCUA
.(..(.....)..)...(((..(((.((....)).)))..)))...(((.((((((.((((((((((...(((....)))...))------)))))))).)))))).))). ( -40.20)
>consensus
ACGACGAGGAGGAGGAGGCGGAUGCUG_________CGGAUGCGGAGGCGGCUGUACUUGCAUUUGCUAAUGCGGAUGCAGAU____________GCGGAUGCAUUGGCUA
................(((.(((((...........(((.(((....))).)))...((((((((((....))))))))))....................))))).))). (-25.30 = -25.62 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:34 2006